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Large-scale SNP discovery through RNA sequencing and SNP genotyping by targeted enrichment sequencing in cassava (Manihot esculenta Crantz)
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Metadata
Document Title
Large-scale SNP discovery through RNA sequencing and SNP genotyping by targeted enrichment sequencing in cassava (Manihot esculenta Crantz)
Author
Pootakham W., Shearman J.R., Ruang-Areerate P., Sonthirod C., Sangsrakru D., Jomchai N., Yoocha T., Triwitayakorn K., Tragoonrung S., Tangphatsornruang S.
Name from Authors Collection
Scopus Author ID
56030033100
Scopus Author ID
36059124300
Affiliations
National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani, Thailand; Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
Type
Article
Source Title
PLoS ONE
ISSN
19326203
Year
2014
Volume
9
Issue
12
Open Access
All Open Access, Gold, Green
Publisher
Public Library of Science
DOI
10.1371/journal.pone.0116028
Format
Abstract
Cassava (Manihot esculenta Crantz) is one of the most important crop species being the main source of dietary energy in several countries. Marker-assisted selection has become an essential tool in plant breeding. Single nucleotide polymorphism (SNP) discovery via transcriptome sequencing is an attractive strategy for genome complexity reduction in organisms with large genomes. We sequenced the transcriptome of 16 cassava accessions using the Illumina HiSeq platform and identified 675,559 EST-derived SNP markers. A subset of those markers was subsequently genotyped by capture-based targeted enrichment sequencing in 100 F1 progeny segregating for starch viscosity phenotypes. A total of 2,110 non-redundant SNP markers were used to construct a genetic map. This map encompasses 1,785 cM and consists of 19 linkage groups. A major quantitative trait locus (QTL) controlling starch pasting properties was identified and shown to coincide with the QTL previously reported for this trait. With a high-density SNP-based linkage map presented here, we also uncovered a novel QTL associated with starch pasting time on LG 10. © 2014 Pootakham et al.
Industrial Classification
Knowledge Taxonomy Level 1
Knowledge Taxonomy Level 2
License
N/A
Rights
N/A
Publication Source
Scopus